Configuration

S-Cap (Smith and Kitzman 2023)

S-Cap (Smith and Kitzman 2023) as run in the cited comparison.

Overview

S-Cap (Smith and Kitzman 2023) as run in the cited comparison.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

6 evaluations · 22 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: BRCA1 saturation genome editing, synonymous and intronic SNVs: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: BRCA1 saturation genome editing, synonymous and intronic SNVs (Smith and Kitzman benchmark set)	0.955 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on BRCA1 saturation genome editing, synonymous and intronic SNVs splicing-follow-up-20261009-protocol-smith2023-brca1-sge-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell B3; row S-Cap, column BRCA1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: BRCA1 saturation genome editing, synonymous and intronic SNVs: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: BRCA1 saturation genome editing, synonymous and intronic SNVs (Smith and Kitzman benchmark set)	1 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on BRCA1 saturation genome editing, synonymous and intronic SNVs splicing-follow-up-20261009-protocol-smith2023-brca1-sge-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell B11; row Exon_S-Cap, column BRCA1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: BRCA1 saturation genome editing, synonymous and intronic SNVs: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: BRCA1 saturation genome editing, synonymous and intronic SNVs (Smith and Kitzman benchmark set)	0.953 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on BRCA1 saturation genome editing, synonymous and intronic SNVs splicing-follow-up-20261009-protocol-smith2023-brca1-sge-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell B19; row Intron_S-Cap, column BRCA1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: BRCA1 saturation genome editing, synonymous and intronic SNVs: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: BRCA1 saturation genome editing, synonymous and intronic SNVs (Smith and Kitzman benchmark set)	0.896 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on BRCA1 saturation genome editing, synonymous and intronic SNVs splicing-follow-up-20261009-protocol-smith2023-brca1-sge-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell B27; row Intron_NonCanon_S-Cap, column BRCA1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: FAS exon 6 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: FAS exon 6 saturation MPSA (Smith and Kitzman benchmark set)	0 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on FAS exon 6 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-fas-exon6-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell C3; row S-Cap, column FAS
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: FAS exon 6 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: FAS exon 6 saturation MPSA (Smith and Kitzman benchmark set)	0 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on FAS exon 6 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-fas-exon6-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell C11; row Exon_S-Cap, column FAS
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.836 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D3; row S-Cap, column MLH1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D11; row Exon_S-Cap, column MLH1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.874 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D19; row Intron_S-Cap, column MLH1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.517 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D27; row Intron_NonCanon_S-Cap, column MLH1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: MST1R (RON) exon 11 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MST1R (RON) exon 11 saturation MPSA (Smith and Kitzman benchmark set)	0.133 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on MST1R (RON) exon 11 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-mst1r-exon11-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell F3; row S-Cap, column RON
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: MST1R (RON) exon 11 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MST1R (RON) exon 11 saturation MPSA (Smith and Kitzman benchmark set)	0.116 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on MST1R (RON) exon 11 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-mst1r-exon11-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell F11; row Exon_S-Cap, column RON
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: MST1R (RON) exon 11 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MST1R (RON) exon 11 saturation MPSA (Smith and Kitzman benchmark set)	0.142 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on MST1R (RON) exon 11 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-mst1r-exon11-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell F19; row Intron_S-Cap, column RON
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: MST1R (RON) exon 11 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MST1R (RON) exon 11 saturation MPSA (Smith and Kitzman benchmark set)	0.0763 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on MST1R (RON) exon 11 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-mst1r-exon11-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell F27; row Intron_NonCanon_S-Cap, column RON
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: POU1F1 exon 2 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: POU1F1 exon 2 saturation MPSA (Smith and Kitzman benchmark set)	0.216 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on POU1F1 exon 2 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-pou1f1-exon2-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell E3; row S-Cap, column POU1F1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: POU1F1 exon 2 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: POU1F1 exon 2 saturation MPSA (Smith and Kitzman benchmark set)	0.182 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on POU1F1 exon 2 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-pou1f1-exon2-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell E11; row Exon_S-Cap, column POU1F1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: POU1F1 exon 2 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: POU1F1 exon 2 saturation MPSA (Smith and Kitzman benchmark set)	0.231 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on POU1F1 exon 2 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-pou1f1-exon2-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell E19; row Intron_S-Cap, column POU1F1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: POU1F1 exon 2 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: POU1F1 exon 2 saturation MPSA (Smith and Kitzman benchmark set)	0 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on POU1F1 exon 2 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-pou1f1-exon2-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell E27; row Intron_NonCanon_S-Cap, column POU1F1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: WT1 exon 9 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: WT1 exon 9 saturation MPSA (Smith and Kitzman benchmark set)	0.952 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on WT1 exon 9 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-wt1-exon9-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell G3; row S-Cap, column WT1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: WT1 exon 9 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: WT1 exon 9 saturation MPSA (Smith and Kitzman benchmark set)	0.9 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on WT1 exon 9 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-wt1-exon9-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell G11; row Exon_S-Cap, column WT1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: WT1 exon 9 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: WT1 exon 9 saturation MPSA (Smith and Kitzman benchmark set)	0.969 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on WT1 exon 9 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-wt1-exon9-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell G19; row Intron_S-Cap, column WT1
Configuration: S-Cap (Smith and Kitzman 2023)	Protocol: WT1 exon 9 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: WT1 exon 9 saturation MPSA (Smith and Kitzman benchmark set)	0.95 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source S-Cap on WT1 exon 9 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-wt1-exon9-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell G27; row Intron_NonCanon_S-Cap, column WT1

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Benchmarking splice variant prediction algorithms using massively parallel splicing assays · Original source · Genome Biology 24:294, published 2023-12-21; PMC10734170 full-text XML
Smith and Kitzman 2023, Additional file 3 (Table S2) · Original source · 13059_2023_3144_MOESM3_ESM.xlsx inside the Europe PMC supplementaryFiles zip for PMC10734170

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Technical metadata and extraction receipts

Stable ID: splicing-follow-up-20261009-config-smith2023-s-cap

areas: dna-genomes
contexts: research
method types: supervised_machine_learning
reported name: S-Cap (Smith and Kitzman 2023)
foundation model eligible: false
missing metadata: version: reason: unreported; note: Precomputed 'sens' scores; version not printed
parameters: Most severe of the dominant and recessive models at essential splice sites; transformed to 1 - score. Transcriptome-normalised threshold calling 10% of 500,000 background SNVs: 0.387096774194 (Table S2 'Thresholds' column C)
source locator: Methods 'Scoring with eight splice effect predictors'; Additional file 3 'Thresholds'
limitations: S-Cap scores only some synonymous variants and variants within 50 bp of a splice site: 61.0% of the background set was unscored, so its threshold comes from the scored part of the background.

Related records

configuration of: S-Cap
system: S-Cap on BRCA1 saturation genome editing, synonymous and intronic SNVs
system: S-Cap on FAS exon 6 saturation MPSA
system: S-Cap on MLH1 curated clinical splicing variants
system: S-Cap on MST1R (RON) exon 11 saturation MPSA
system: S-Cap on POU1F1 exon 2 saturation MPSA
system: S-Cap on WT1 exon 9 saturation MPSA

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